Mercurial > repos > mvdbeek > docker_toolfactory_alpha
comparison Dockerfile @ 0:7e0392d4531c
Initial Commit.
| author | m.vandenbeek@gmail.com |
|---|---|
| date | Tue, 02 Dec 2014 15:14:12 +0100 |
| parents | |
| children | 5b930e77b1f3 |
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| -1:000000000000 | 0:7e0392d4531c |
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| 1 # Toolfactory image | |
| 2 # | |
| 3 # VERSION 0.1 | |
| 4 | |
| 5 FROM debian:jessie | |
| 6 | |
| 7 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com | |
| 8 | |
| 9 # make sure the package repository is up to date | |
| 10 RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update | |
| 11 | |
| 12 # Install all requirements that are recommend by the Galaxy project | |
| 13 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y autoconf | |
| 14 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y automake | |
| 15 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential | |
| 16 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y gfortran | |
| 17 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y cmake | |
| 18 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y git-core | |
| 19 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libatlas-base-dev | |
| 20 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libblas-dev | |
| 21 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y liblapack-dev | |
| 22 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y mercurial | |
| 23 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y subversion | |
| 24 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-dev | |
| 25 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y pkg-config | |
| 26 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y openjdk-7-jre | |
| 27 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-setuptools | |
| 28 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y adduser | |
| 29 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y python-virtualenv | |
| 30 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y zlib1g-dev | |
| 31 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libfreetype6-dev | |
| 32 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y ghostscript | |
| 33 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base-core | |
| 34 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y imagemagick | |
| 35 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y graphicsmagick-imagemagick-compat | |
| 36 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y exonerate | |
| 37 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y bedtools | |
| 38 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y wget | |
| 39 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y curl | |
| 40 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libcurl4-openssl-dev | |
| 41 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libssl-dev | |
| 42 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libreadline-dev | |
| 43 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libxml2-dev | |
| 44 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y samtools | |
| 45 | |
| 46 RUN DEBIAN_FRONTEND=noninteractive easy_install numpy | |
| 47 RUN DEBIAN_FRONTEND=noninteractive easy_install pysam | |
| 48 RUN DEBIAN_FRONTEND=noninteractive easy_install tornado | |
| 49 RUN DEBIAN_FRONTEND=noninteractive easy_install matplotlib | |
| 50 RUN DEBIAN_FRONTEND=noninteractive easy_install pycurl | |
| 51 RUN DEBIAN_FRONTEND=noninteractive easy_install pip | |
| 52 RUN DEBIAN_FRONTEND=noninteractive pip install metaseq | |
| 53 RUN DEBIAN_FRONTEND=noninteractive easy_install pandas | |
| 54 RUN DEBIAN_FRONTEND=noninteractive pip install ipython | |
| 55 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y zlib1g-dev | |
| 56 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y liblzma-dev | |
| 57 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libpcre3-dev | |
| 58 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libbz2-dev | |
| 59 RUN DEBIAN_FRONTEND=noninteractive pip install rpy2 | |
| 60 | |
| 61 RUN Rscript -e 'install.packages("latticeExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")' | |
| 62 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq2")' | |
| 63 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq")' | |
| 64 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR")' | |
| 65 RUN Rscript -e 'install.packages("ggplot2", dependencies=TRUE, repos="http://cran.us.r-project.org")' | |
| 66 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("EDASeq")' | |
| 67 RUN Rscript -e 'install.packages("reshape", dependencies=TRUE, repos="http://cran.us.r-project.org")' | |
| 68 RUN Rscript -e 'install.packages("gridExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")' | |
| 69 | |
| 70 | |
| 71 RUN adduser galaxy -u 1002 | |
| 72 | |
| 73 #VOLUME ["/home/galaxy/"] | |
| 74 #RUN chown -R galaxy /home/galaxy/ ##Doesn't work on volumes | |
| 75 RUN mkdir /home/galaxy/job_working_directory | |
| 76 WORKDIR /home/galaxy/job_working_directory | |
| 77 USER galaxy | |
| 78 | |
| 79 | |
| 80 #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy | |
| 81 CMD /bin/bash |